mosaik-aligner installation problem on redhat 6

[joachim.jacob]

Hi,

I have downloaded the Mosaik-1.1.0021-source.tar.bz2 on our RedHat6 64 bit system. When running 'make' in the src directory, errors occur. Dependencies (gcc-c++, zlib, zlib-devel) have caused the some of the errors, but now I am stuck.

Anybody to put me on the right track?

$ make
Building MOSAIK for the following platform: linux
=========================================================
- Building in CommonSource
- Building in AssemblyFormats
make[2]: Nothing to be done for `all'.

- Building in DataStructures
make[2]: Nothing to be done for `all'.

- Building in ExternalReadFormats
make[2]: Nothing to be done for `all'.

- Building in MosaikReadFormat
make[2]: Nothing to be done for `all'.

- Building in PairwiseAlignment
make[2]: Nothing to be done for `all'.

- Building in Utilities
make[2]: Nothing to be done for `all'.


- Building in MosaikBuild
  * linking MosaikBuild
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make[1]: *** [MosaikBuild] Error 1

- Building in MosaikAligner
  * linking MosaikAligner
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikAligner] Error 1

- Building in MosaikSort
  * linking MosaikSort
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikSort] Error 1

- Building in MosaikMerge
  * linking MosaikMerge
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikMerge] Error 1

- Building in MosaikAssembler
  * linking MosaikAssembler
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikAssembler] Error 1

Thanks in advance!

[Thomas Doktor]

Look here for a solution to "-lpthread": http://www.justlinux.com/forum/showthread.php?t=126349

"-lz" is the zlib which you have installed. Is the Mosaik buildprocess looking in the right folder?

You can always just google "/usr/bin/ld: cannot find lpthreads" (or whatever library it's missing) for these kinds of things.

[joachim.jacob]

Sorry, I can't solve the problem

Hi,

Thanks for your suggestion to google: that is a new approach.

zlib is installed, but I am not sure about lpthreads.

I am learning now about 'ldconfig': apparently this is used to create links to the most up-to-date libraries. Perhaps I should pass a parameter over there.

Quitting mosaik for now.

[austic]

library issue (to some extent)

I am having the same problem. ("/usr/bin/ld: cannot find -lpthread")
upgraded my glibc using the add/remove software interface (awesome!) worked great
then, like you i got the "/usr/bin/ld: cannot find -lz" error
came across this:
http://stackoverflow.com/questions/3...cannot-find-lz
which would seem to suggest there's something wrong with the Makefile.in
However, I looked through several of the Makefile.in and header files for each of the modules and couldn't find anything overtly wrong (plus, i highly doubt the author would release it if it didn't compile). So I started looking around some more and found this:

http://linux.digitalsp.com/2007/12/compile-error-usrbinld-cannot-find-lz.html

i went to my add/remove software interface and searched for zlib1g-dev but couldn't find any package named that, however i *did* find several packages with "zlib" included in the name. so i downloaded them all:
mingw32-zlib
perl-IO-Zlib (<--- this was probably the one)
perl-Archive-Tar
mingw32-zlib-static
jzlib
jzlib-javadoc
zlib-static (<-- or maybe this one)
jzlib-demo

and then the code would compile

[PRoebuck]

RHEL 6.0

I got source distribution to compile/link by modifying the 'includes/linux.inc' as follows:

# define our processor specific flags
export PLATFORM_FLAGS = -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -static
export PLATFORM_LIBS = -L/usr/lib/x86_64-redhat-linux5E/lib64

Determine library location (PLATFORM_LIBS) with command:
$ find /usr/lib -name "*pthread*"

Needs an exact match to 'libpthread.a".

The GNU_SOURCE define solved linker error for MosaikAlign complaint about C99 version of fscanf().

[Carlos Borroto]

zlib-static (<-- or maybe this one)

I was also hit by this issue. I'm using CentOS 6.4. With the help of this thread I was able to solve it by installing these two packages:

sudo yum install zlib-static glibc-static

No need to modify any source files in my case.

Best,
Carlos